"We're all cognizant of the point that we have a long way to go," Matheny said. "Giving them a day [off] like this has a lot of positives. We're not going to abuse them or ride them when they're doing well."
Freese is batting .444 with three home runs and a Major-League leading 10 hits and 12 RBIs through six games. David Descalso started at third and batted sixth in place of Freese.
"The day off is more of a mental break than anything else," Matheny said. "Gives them a chance to shut their brain down and shut the intensity down for a day."
Other lineup changes on Wednesday included Tyler Greene playing second, Erik Komatsu in right, and Matt Carpenter starting at first base and batting cleanup.
"I don't have a lot of hesitation putting him where we need him," Matheny said of Carpenter. "He gives us good at-bats."